Running OWL2Neo4J

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Requirements

• Neo4J up and running
• An OWL ontology

Import an ontology

$ java -jar ./owl2neo4j.jar \
       -o pizza.owl \
       -n "Pizza Ontology" \
       -a PO

Full interface

usage: java -jar owl2neo4j.jar -a <String> [--eqp <String>] [-h] -n
       <String> -o <Path> [-p <String>] [-s <URL>] [-u <String>] [-v]
       [--version]
Import OWL into Neo4J as a labeled property graph.

 -a,--abbreviation <String>   Ontology abbreviation (E.g. GO)
    --eqp <String>            Existential quantification property (E.g.
                              http://www.co-ode.org/ontologies/pizza/pizza
                              .owl#hasTopping)
 -h,--help                    Shows this help
 -n,--name <String>           Ontology name (E.g. Gene Ontology)
 -o,--owl <Path>              Path to OWL file
 -p,--password <String>       Neo4J user password
 -s,--server <URL>            Neo4J server root URL [Default:
                              http://localhost:7474]
 -u,--user <String>           Neo4J user name
 -v,--verbosity               Verbose output
    --version                 Show version

Below you find some more detailed explanation for a few options that might not be self-explanatory.

Options:

• -a / --abbreviation A short abbreviation of the ontology, similar to a prefix or OBO's IDSPACE. Note that the abbreviation will always be converted into upper case letters.
• --eqp Existencial quantification property are a way to define sub class relations in OWL. The script allows to extract one direct existencial quantification at a time.

Importing large ontologies:

By default the OWLAPI XML loader has a 64,000 triple limit. To increase the limit and being able to import larger ontologies start owl2neo4j.jar with DentityExpansionLimit=<LARGE_NUMBER> flag like so:

$ java -jar -DentityExpansionLimit=10000000 owl2neo4j.jar \
    -o extra-large-pizza.owl \
    -n "Extra Large Pizza Ontology" \
    -a ELPO \